How can I stop our Spamassassin from marking all internal emails as spam (sent from a domain on the server to another domain on the server)?

The easiest way to do this, would be to modify /etc/mail/spamassassin and set the trusted_networks setting. You should include localhost, and either your servers IP, or the entire range of IP's that are on your server. If your servers IP address was 1.2.3.4, an example would be:trusted_neteworks 127.0.0.1 1.2.3.4